MemoteReportApp

Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

100.0%

Charge Balance

95.6%

Metabolite Connectivity

100.0%

Unbounded Flux In Default Medium

58.0%

Sub Total

93%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$(95.62 + 57.97 + (3 * 100) + )/((5 * 100)) = 93.37$

Annotation - Metabolites

Presence of Metabolite Annotation

99.9%

Metabolite Annotations Per Database

pubchem.compound

0.0%

kegg.compound

78.5%

seed.compound

99.9%

inchikey

71.1%

inchi

71.1%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

98.9%

bigg.metabolite

65.6%

biocyc

67.4%

Metabolite Annotation Conformity Per Database

pubchem.compound

0.0%

kegg.compound

96.0%

seed.compound

99.9%

inchikey

100.0%

inchi

100.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

99.9%

bigg.metabolite

100.0%

biocyc

99.6%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

78%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$(99.94 + 78.48 + 99.94 + 71.05 + 71.05 + 98.87 + 65.64 + 67.40 + 95.99 + 99.94 + 99.94 + 99.63 + (4 * 100) + (8 * 0))/((24 * 100)) = 78.35$

Annotation - Reactions

Presence of Reaction Annotation

99.8%

Reaction Annotations Per Database

rhea

46.5%

kegg.reaction

62.5%

seed.reaction

92.5%

metanetx.reaction

90.9%

bigg.reaction

53.4%

reactome

0.0%

ec-code

82.6%

brenda

0.0%

biocyc

48.1%

Reaction Annotation Conformity Per Database

rhea

100.0%

kegg.reaction

99.9%

seed.reaction

99.9%

metanetx.reaction

100.0%

bigg.reaction

98.1%

reactome

0.0%

ec-code

96.8%

brenda

0.0%

biocyc

100.0%

Uniform Reaction Identifier Namespace

98.1%

Sub Total

82%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$(99.82 + 46.45 + 62.49 + 92.55 + 90.94 + 53.43 + 82.65 + 48.06 + 99.94 + 99.94 + 98.09 + 96.84 + 98.09 + (3 * 100) + (4 * 0))/((20 * 100)) = 82.02$

Annotation - Genes

Presence of Gene Annotation

99.9%

Gene Annotations Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

64.2%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

100.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

39%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$(99.92 + 64.24 + (1 * 100) + (18 * 0))/((21 * 100)) = 38.78$

Annotation - SBO Terms

Metabolite General SBO Presence

99.7%

Metabolite SBO:0000247 Presence

99.7%

Reaction General SBO Presence

99.4%

Metabolic Reaction SBO:0000176 Presence

99.6%

Transport Reaction SBO:0000185 Presence

98.6%

Exchange Reaction SBO:0000627 Presence

98.3%

Demand Reaction SBO:0000628 Presence

100.0%

Sink Reactions SBO:0000632 Presence

100.0%

Gene General SBO Presence

99.9%

Gene SBO:0000243 Presence

99.9%

Biomass Reactions SBO:0000629 Presence

100.0%

Sub Total

100%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$(99.69 + 99.69 + 99.40 + 99.57 + 98.62 + 98.33 + 99.92 + 99.92 + (3 * 100) + )/((11 * 100)) = 99.56$

Total Score

91%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$((3 * 93.37) + (1 * 78.35) + (1 * 82.02) + (1 * 38.78) + (2 * 99.56))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 90.90$

Total Score

91%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

FBC enabled

Errored

Basic Information

Model Identifier

iMK1317

The MIRIAM guidelines require a model to be identified via an ID. Further, the ID will be displayed on the memote snapshot report, which helps to distinguish the output clearly. Implementation: Check if the cobra.Model object has a non-empty "id" attribute, this value is parsed from the "id" attribute of the <model> tag in the SBML file e.g. <model fbc:strict="true" id="iJO1366">.

The model ID is iMK1317

Total Metabolites

1,589

Total Reactions

1,677

Total Genes

1,317

Total Compartments

Metabolic Coverage

1.27

Metabolite Information

Unique Metabolites

1,567

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

1,406

Purely Metabolic Reactions with Constraints

Transport Reactions

145

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

0.39

Reactions With Partially Identical Annotations

0.00

Duplicate Reactions

0.00

Reactions With Identical Genes

0.68

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

Fraction of Transport Reactions without GPR

0.08

Enzyme Complexes

839

Biomass

Biomass Reactions Identified

Biomass Consistency

Errored

Biomass Production In Default Medium

0.50

Unrealistic Growth Rate In Default Medium

false

Biomass Production In Complete Medium

103.09

Blocked Biomass Precursors In Default Medium

Blocked Biomass Precursors In Complete Medium

Ratio of Direct Metabolites in Biomass Reaction

0.10

Number of Missing Essential Biomass Precursors

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

false

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

686

Orphan Metabolites

Dead-end Metabolites

Stoichiometrically Balanced Cycles

397

Metabolite Production In Complete Medium

771

Metabolite Consumption In Complete Medium

798

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

232

Rank

1357

Degrees Of Freedom

320

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.10

Platform Linux

Memote Version 0.10.2

Package Versions